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Model-Based Mediation System with Domain Maps for Brain Data Integration

Explore the cerebellar distribution of rat proteins with high homology to human NCS-1 and other rodents using a semantic mediation system. This system integrates data, relationships, and constraints using structural constraints and domain maps. Utilize semantic road maps for intuitive browsing of source data and integrated views across multiple worlds.

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Model-Based Mediation System with Domain Maps for Brain Data Integration

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  1. An Extensible Model-Based Mediator System with Domain Maps Amarnath Gupta* Bertram Ludäscher* Maryann E. Martone+ *San Diego Supercomputer Center (SDSC) +National Center for Microscopy and Imaging Research (NCMIR) University of California, San Diego (UCSD)

  2. Surface atlas, Van Essen Lab stereotaxic atlas LONI  MODEL-BASED Mediation MCell, CNL, Salk CCB, Montana SU NCMIR, UCSD Federation of Brain Data using Model-Based Medition Result (XML/XSLT) PROTLOC Result (VML) ANATOM

  3. ??? Integrated View ??? ??? Integrated View Definition ??? ???Mediator ??? The Need for Semantic Integration Cross-source queries What is the cerebellar distribution of rat proteins with more than 70% homology with human NCS-1? Any structure specificity? How about other rodents? Cross-source relationships are modeled Semantic (knowledge-based) mediation services Data, relationships, constraints are modeled (CMs) Wrapper Wrapper Wrapper Wrapper Web protein localization morphometry neurotransmission CaBP, Expasy

  4. Integrated-DTD := XML-QL(Src1-DTD,...) DOMAIN MAP IF  THEN  IF  THEN  IF  THEN  Structural Constraints (DTDs), Parent, Child, Sibling, ... A = (B*|C),D B = ... . . .... .... .... .... (XML) Objects Raw Data Raw Data ConceptualModels Raw Data XML-Based vs. Model-Based Mediation CM ~ {Descr.Logic, ER, UML, RDF/XML(-Schema), …} CM-QL ~ {F-Logic, OIL, DAML, …} Integrated-CM := CM-QL(Src1-CM,...) Logical Domain Constraints No Domain Constraints Classes, Relations, is-a, has-a, ... C1 C2 R C3 XML Elements XML Models

  5. Model-Based Mediation with DOMAIN MAPS (DMs) • “Semantic Road Maps” for situating source data • => navigational aid (browsing source classes at the conceptual level) • => basis for integrated views across multiple worlds • => link points (concepts) and labeled arcs (roles) • => formal semantics (in FL and/or DLs) • Example: ANATOM DM • = antatomical entities (concepts) + is_a, has_a, overlaps, ... (roles) • => from syntactic equality to semantic joins LINK(X,Y): X.zip =Y.zip X.addr in Y.zip X.zip overlaps Y.county ... Integrated-CM(Z1,...) := get X1,... from Src1; get X2,... from Src2; LINK (Xi, Yj); Zj = CM-QL(X1,...,Y1,...)

  6. ANATOM Domain Map

  7. ANATOM Domain Map with Registered Data ANATOM DATA

  8. Integrated View Definition DERIVE protein_distribution(Protein, Organism, Brain_region, Feature_name, Anatom, Value) FROM I:protein_label_image[ proteins ->> {Protein}; organism -> Organism; anatomical_structures ->> {AS:anatomical_structure[name->Anatom]}] , % from PROLAB NAE:neuro_anatomic_entity[name->Anatom; % from ANATOM located_in->>{Brain_region}], AS..segments..features[name->Feature_name; value->Value]. • provided by the domain expert and mediation engineer • declarative language (here: F-logic) Query Processing

  9. PROTLOC-AxioMap Client-Side Result Visualization(using AxioMap Viewer: Ilya Zaslavsky)

  10. FL rule proc. LP rule proc. Model-Based Mediator Prototype USER/Client CM (Integrated View) Domain Map DM Mediator Engine Integrated View Definition IVD XSB Engine Graph proc. GCM GCM GCM CM S1 CM S2 CM S3 CM Plug-In CM Queries & Results (exchanged in XML) Logic API (capabilities) CM-Wrapper CM-Wrapper CM-Wrapper XML-Wrapper XML-Wrapper XML-Wrapper S3 S1 S2

  11. Mediation Services: Semantic Annotation Toolsline drawing =annotate=> (spatial) DB for mediation

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